Pokemon Amethyst
by Thireven
Summary: Shu Hagi moved to the Hoenn region to find peace and quiet. However, when an old friend returns, he takes up the mantle of Pokemon Trainer once again to set out on a journey to become Champion-and possibly do more.
1. Prologue

Please note that this story will contain several darker subjects, as evident of this prologue. If dark subjects do not set well with you, turn away now while you still can. While the story itself won't contain anything quite as serious, some of it may unsettle you. I don't want to hear complaints if you read this and don't like it, because I have warned you.

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It was exceedingly rare for someone to move away from the Johto region. Unlike the Kanto region, it was generally a quiet and peaceful place, despite the annual Pokemon tournament and the occasional criminal. The antics of Team Rocket had been the first threat the region had faced in a few decades, a sign of the fact the region wasn't as prone to crimes as their neighbors. However, concerning the person who had recently moved to the Hoenn region and his connection with one of the most sickening crimes recorded in the Johto region, his reasoning for moving had been understandable.

While the exact role this trainer played in this crime is unknown, he was related to the criminal as the man's son.

Vincent Richard Hagi was a renowned scientist, well-known for his research and discoveries concerning the relationship between the DNA of Pokemon and Humans. After several years of research, he came to conclusion that it was possible to take DNA from a Pokemon and implant it into that of a young human child. Attempt after attempt failed, and finally, after discovering the discarded bodies of the children he had used, he was charged for a crime against humanity. Ultimately, however, he vanished, never to be seen again.

The whereabouts of his son had been unknown for several years following his disappearance as a toddler. Though he had not been found among the dead, investigators assumed he had died along with the other children Vincent had experimented on. However, more than half a decade later, a Trainer stumbled upon the missing child out in the wilds of Mt. Silver, living with a small family of Ursaring and Teddiursa. The Nurse Joy residing at the base of the mountain took up his reintroduction to society, and so began a rough year of teaching the boy how to once again live among the humans.

It wasn't until age fifteen that Shu Hagi decided to become a Pokemon Trainer. It was at this time that Team Rocket first began running their operation in the Johto region. Lightning Yumachi, a Trainer hailing from the Kanto Region, had traveled to the Johto region at this time to begin a new journey. The two first met in Celadon, ready to challenge the gym. They became fast friends, traveling together.

After successfully stopping Team Rocket with the help of Gold and his rival Silver, Lightning went on to challenge the Indigo League, successfully beating the Elite Four and becoming the champion. It was soon afterwards that Shu ultimately moved away to the Hoenn region, seeking a quiet life.


	2. Chapter 1

_Two years later - Hoenn_

Another day came in the town of Littleroot, as the sun once again rose into the brightening sky to shine light upon the buildings. A Pidgey flew ahead, chirping happily at the day's beginning. Residents of the small town rose with the sun to begin their day, setting off to work or to do their daily chores.

However, for one of the town's most recent inhabitants, the sunshine and cries of the morning Pokemon did not serve to wake him from his dreams…

"_Let's battle!" The girl declared, long black hair whipping around her face as the wind picked up. "One-on-one, no substitutions."_

The raven-haired teenager known was Shu Hagi was lying sprawled on his bed, one arm draped across his torso, the other dangling over the side of his bed. His blanket sat crumpled halfway off the end of the bed, his legs spread out. Both the white shirt he wore was creased up to reveal his stomach.

"_Sure thing, Lightning. I won't be going easy on you," Shu replied, a small smirk tugging at his lips._

A small, brown Pokemon was resting on a pile of clothes near the bed, amber eyes partly opened to stare at the hand hanging near the floor as it twitched.

_Both lowered their hands to their belts, where their PokeBalls sat attached to them. With a shift moment, Shu unhooked of the balls and tossed it into the air. Lightning was seconds behind, throwing a PokeBall of her own towards the sky. The red light that burst from hers formed into a tall, furred creature in front of her. Flames sprouted from the back of his neck, flaring as he snorted. Shu's PokeBall released a large, blue crocodilian Pokemon that snapped her teeth, eyeing the mammal in front of her. _

"_Let's see if your Typhlosion can beat Chopper," Shu said, chuckling._

"_As if that Feraligatr of yours could defeat Flare," Lightning replied._

The sleeping male grunted, rolling over onto his side and shifting so his arm was lying on the bed at his side. After a few moments, the Pokemon stood, stretching out her legs and shaking. She leaped onto the nightstand, staring at Shu with brown eyes.

"_Look out!" Lightning snapped._

_Flare dodged, rolling across the ground as a stream of water raced through the air where he had been. The Typhlosion looked up, growling, as the Feraligatr let out what could have been a chuckle. Gritting his teeth in annoyance, Flare stood, glancing back at his trainer for instructions._

_Shu raised his hand to point at the Typhlosion, shouting, "Hydro Pump, Chopper!"_

The Eevee tilted her head to this side before letting out a small mew. Shu had rolled over to lay on his back once again. Crouching, stretching her hind legs out, she eyed her target. With a bound forward, she leaped through the air and landed on the teenager's stomach. The raven haired boy let out an 'oomph' as his grey-blue eyes snapped open. Fully awake, he glared down at the culprit, who promptly slid down to rest at his side. Sighing, he sat up, placing his hand on her head.

"What was that all about?" He asked. "You're not hungry, are you?"

"Eev!" She purred, happily.

She leaned into his hand and he moved to scratch her cheek, a light-hearted smile on his face.

After a moment, he picked her up and placed her onto the floor. Yawning and stretching his arms up, he stood. Eyeing his room, he sighed and kicked the pile of dirty clothes before heading for his dresser. Casually tossing uninteresting clothes onto his bed, he dug through the draws until finding his grey tank top and black jeans. Shrugging, he pulled off his current shirt, dropping it onto the top of the dirty clothes on the floor. He tugged the tank top on, and then set to pull on his pants. As his foot decided to get stuck in the second pant leg, he growled and began to hop up and down until he was finally able to get it on. With a huff, he zipped it up, buttoned it, and set to finding his socks.

His Eevee popped her head out from underneath the bed, a pair of white socks clenched firmly in her teeth. Chuckling, he waited until she scooted herself to his feet before sitting down. She immediately dropped the socks once he lowered his hand. He tugged them on, then slipped his feet into his boots on tied them.

"Well, Gem, let's get some breakfast in you," he declared, swooping down to scoop her into his arms.

"Vee!"

Shu grinned as he trudged down the stairs, boots thumping loudly against the wooden floorboards. As soon as his foot touched down on the first floor of the house, there was a knock at the door. Groaning at the interruption, he trudged walked forward to the front door and reached out to swing it inward.

"Yes- Oh, Professor Burch."

The Professor grinned, scratching at his beard as a soft breeze ruffled his messy brown hair. His other hand was tucked into the pocket of his white lab coat. Several moments of silence passed before Burch coughed into his fist.

"May I talk with you?" He asked cheerily.

"Can it be over breakfast?" Shu replied.

"That would be wonderful!" Burch stated.

"You haven't eaten yet, have you?" Shu muttered, moving to let the Professor in. "Alright, I'll whip something up."

He trailed into the kitchen after Burch, who slipped into one of the chairs at the table.

Daring a glance into the fridge, Shu sighed, finding nothing but a gallon of milk and bottles of water stashed into the machine. Closing the door, he reached up and flung open the cupboards. A lone box of cereal sat there, surrounded by cups, bowls, and spoons. Upon checking the expiration date on the top of the box, he found himself muttering under his breath. He dug out two cups and set them down on the counter. He snorted as he opened the cabinets below, pulling out Gem's water dish, which he sat down near the cups. Rubbing his head, Shu swung the door to the fridge open to grab the milk. He twisted off the cap and poured the white liquid into the cups, kneeled to pour some into the dish. Hr quickly capped it, shoved it into the fridge and closed the door, then grabbed the glass.

He sat down beside the professor, handing the older male one of the cups. Burch accepted it, taking a sip out of it.

"Did you forget to go shopping again?" Burch questioned when Shu sat down heavily.

"Yes," the teenager grunted. "What was it that you wanted to talk about?"

"Ah, yes! I received an email early this morning- very early, infact- from Lightning. She and Professor Oak will be arriving in the Hoenn region soon!"

Shu choked on the milk he was drinking, letting out a strained cough as he finally swallowed it. Setting down the cup, he slowly turned to look at Burch with a mixture of unease and surprise.

"Lightning is…coming here?"

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A/N: These chapters will be incredibly short, fair warning. I doubt there will be many that get over two thousand words. Okay, back to CW.


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